# User:TheLarry/Notebook/Larrys Notebook/2009/10/21

Writing the Paper Main project page
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## Outline

I have like three references for other dynamic models. I am pretty happy with a couple of sentences that i can say on them especially a nice quote from Gillespie about stochastic models for chemical reactions.

While fixing up the outline for results, i said this model can check to see which states are entered the most. So i wrote a sub.vi that will count the number of times each state was entered. This was annoying since it had to figure out what each state was. I was able to do it by making a .vi that will construct every possible state (128 of them) and then used an equal condition to the present state to figure it out. Any way i am pretty proud of it. I can now graph which states are entered the most, and many of them are not entered at all. Using this I can figure out the core cycle for this experimental condition. And what was the state when it detached from the microtubule. I noticed that the sub.vi i wrote takes into account the head order. So i got rid of this with an Or condition--so before it thought Head 1 μ-ATP in front of Head 2 μ-ADP was different from Head 2 μ-ADP behind Head 1 μ-ATP. But i got rid of that problem. There is a redundancy though but i can take care of that later if it is a problem. I left in the separation. It might come in handy later. I am not sure.

So here is what I am talking about. The top image is without the or. So it keeps track of Head 1 and Head 2. The bottom is with the or so it ignores Head 1 and Head 2 labels. The x axis is number of times in each state per entire run. The y axis is an arbitrary number that corresponds to an individual state so μ-ATP/μ-ADP could be number 58 or something like that. I don't have a good way to do the numbering yet. Also I could divide by the average number of steps so i can get number of times in each state per step which could be good information.

I looked through all the most occuring states and the only odd part is the bound ADP-P and unbound ADP occur often. This is understood since the P release is about half as slow as ADP unbinding. So the ADP is unbinding and rebinding before the P is released.

I have a problem with my binning histogram. Right now i have it set to 50 bins distributed evenly. But for states with very few times in it, say like just once this might give NAN for an answer. But if i had like 1 bin or something this might not be a problem. I might have to write something to take a look at these states. But i have half of tomorrow to do that since i'll write in the morning.

I worked on the outline this morning and then wrote the labview code in the afternoon like Evans suggested. I am pretty happy with the outline and think i can start writing the main thing now. I can start tomorrow. The outline is 4 pages long so i assume the paper is going to be pretty long. Koch said he wanted to publish in PLoS One. I am not sure what kind of page restriction they have. But i'll write and trim down if need be later.

Oh yeah i don't have a conclusion yet. I think that'll take the most for Koch and I to discuss. Possibly i can say this simulation kicks ass. Or i might want to look further into our speculation of things like osmotic pressure and shit like that. I am not sure yet.